The oxygenase-catalyzed post-translational hydroxylation of prolyl residues is important for protein function and structure in animals. In the case of collagen, prolyl-4-hydroxylation stabilises the triple helix fold whereas prolyl-3-hydroxylation is thought to destabilise the triple helix fold. More recently, prolyl-4-hydroxylation has been shown to play an important role in the animal hypoxic response by signalling for the proteasomally mediated degradation of the hypoxia inducible transcription factor alpha subunit (HIFα) by enhancing its binding to the targeting component of a ubiquitin ligase. The oxygen dependence of the HIFα prolyl hydroxylases (PHD/EGLN enzymes), in addition to appropriate kinetic properties, is proposed to enable them to act as an oxygen-sensing component for the HIF-based hypoxic response system, which is conserved in all animals and involves transcriptional regulation of multiple genes in a context-dependent manner. Several reports of alternative substrates for the PHDs have emerged but the biological role of these modifications is unclear.
In some animals, including humans, HIF transcriptional activity is also regulated by asparaginyl hydroxylation, which reduces HIF binding to transcriptional coactivator proteins including p300. The HIF asparaginyl hydroxylase (FIH) and the PHDs belong to the ubiquitous family of Fe(II) and 2-oxoglutarate-dependent oxygenases (2OG oxygenases). 2OG oxygenases couple the two-electron oxidation of their ‘prime’ substrate to the oxidative decarboxylation of 2OG to give carbon dioxide (CO2) and succinate.
A number of human 2OG oxygenases are of therapeutic interest including the hypoxia inducible factor prolyl (PHD) and asparaginyl hydroxylases (FIH), the deoxyribonucleic acid demethylases (ALKBHs and FTO), the 5-methylcytosine hydroxylases (TET enzymes), ribonucleic acid hydroxylases (C2ORF60), lysyl hydroxylases (JMJD6), phytanoyl coenzyme A hydroxylase (PAHX), procollagen prolyl and lysyl hydroxylases, and the histone lysyl and arginyl demethylases (JMJ-domain containing enzymes, FBXL11, PHF8).
Following the assignment of the HIF hydroxylases as 2OG oxygenases and the solution of crystal structures for them, several other oxygenases with unknown function were identified by structurally informed bioinformatic analyses. Importantly, the JmjC jumonji-domain-containing oxygenases that bear structural similarity with FIH have been found to catalyze the N-demethylation of Nε-lysyl residues of histones. Further, FIH itself has been found to have multiple substrates from the ankyrin repeat domain family, including transcription factors, and JMJD6 was found to catalyze lysyl 5-hydroxylation of splicing-related proteins. Collectively, these results suggest the presence of multiple regulatory levels and interfaces between oxygen and transcriptional activity, and maybe splicing, which are mediated by 2OG oxygenases.